Coherent interactions of dyes assembled on DNA

The optical behavior of an organized dye assembly is different from that of the isolated dye; this difference is explained using molecular exciton theory. The theory predicts that mutual orientation, the number of dyes in the cluster, and combinations of different dyes should display given characteristic spectroscopic behaviors due to coherent interactions. Comparison of theoretical predictions with experimental results has been limited so far. One of the reasons is the absence of a rigid and well-organized system that can control the orientation and size of the dye assembly. Recently, the DNA duplex has been used to assemble chromophores in a programmed manner. Use of DNA allows organized dye assembly with a given size and particular orientation. In this review, we evaluate the spectroscopic behavior of the H-type aggregate based on molecular exciton theory and compare it with actual dye assembly with DNA duplex. Furthermore, we demonstrate the importance of coherent interactions on the observed optical properties of dyes assembled in a DNA duplex.

► We briefly review the methodology of assembling dyes on a DNA duplex.
► Coherent interaction in homo dye-cluster is demonstrated both from theoretical and experimental points of view.
► Coherent interaction in hetero H-dimers is theoretically and experimentally examined.
► Spectroscopic behavior of intercalated dye is explained from coherent interaction.
► Importance of coherent interaction for efficient quenching of a fluorophore is demonstrated.